[gmx-users] how to assign options of the same type?

Barnett, James W jbarnet4 at tulane.edu
Sun May 24 15:46:05 CEST 2015

If you use -deffnm it gives the same prefix to all files that are output (and requires the same prefix on the .tpr file that is input).

For example, if your tpr file is "md.ttr" you could do

gmx mdrun -deffnm md

Your checkpoint files will be named "md.cpt" and your trr files will be named "md.trr", as well as anything else that is being output as specified in the mdp file you used with grompp (energy files, gro files, xtc files, etc).

James “Wes”​ Barnett
Ph.D. Candidate
Chemical and Biomolecular Engineering

Tulane University
Boggs Center for Energy and Biotechnology, Room 341-B
New Orleans, Louisiana 70118
jbarnet4 at tulane.edu​

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Sunday, May 24, 2015 7:55 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] how to assign options of the same type?

On 5/24/15 8:29 AM, Zhang, Cheng wrote:
> Can I ask how to assign options of the same type?
> For example, on the website of
> http://manual.gromacs.org/current/programs/gmx-mdrun.html
> It is said in the "Synopsis":
> [-o [<.trr/.cpt/...>]
> I want to name the output files as md.trr and md.cpt. However, the followings do not work:
> -o md.trr md.cpt
> -o md.trr/md.cpt
> -o md.trr -o md.cpt
> So do you know what is the syntax?

You can't specify multiple files to any option that is not labeled "Mult."  In
the case of mdrun -o, that is the output trajectory format.  The general help
info in the synopsis indicates that this file type may be interchangeable in a
general sense, but here it is somewhat misleading.  You shouldn't try to output
a checkpoint file in lieu of your trajectory.  The .cpt is produced
(automatically) with -cpo.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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